import argparse
from pathlib import Path
from .delly import DELLY


def main():
    parser = argparse.ArgumentParser(description="ClinSV")
    parser.add_argument("--bam_file", "-in", type=Path, required=True, help="input, bam file, required")
    parser.add_argument("--genome_file", "-genome", type=Path, required=True, help="input, genepred file")
    parser.add_argument("--genome_builder", "-build", type=str, default="hg38", help="input, genome builder")
    parser.add_argument("--genepred_file", "-genepred", type=Path, help="input, genepred file")
    parser.add_argument("--gene_id_file", "-gene_id", type=Path, help="input, gene id file")
    parser.add_argument("--outdir", "-out", type=Path, required=True, help="output, outdir, required")

    parser.set_defaults(func=lambda args: DELLY(**vars(args)).run())
    args = parser.parse_args()
    args.func(args)
